Align Imidazole glycerol phosphate synthase subunit HisH 1; EC 4.3.2.10; IGP synthase glutaminase subunit 1; EC 3.5.1.2; IGP synthase subunit HisH 1; ImGP synthase subunit HisH 1; IGPS subunit HisH 1 (uncharacterized)
to candidate WP_012172228.1 AZC_RS19080 glutamine-hydrolyzing GMP synthase
Query= curated2:Q7MLS3 (204 letters) >NCBI__GCF_000010525.1:WP_012172228.1 Length = 515 Score = 41.2 bits (95), Expect = 3e-08 Identities = 35/114 (30%), Positives = 53/114 (46%), Gaps = 12/114 (10%) Query: 101 VECLGLCDGEVKLLQT--GDLPLPH---MGWNTVSAKAGNPLFKGI-EEGEYFYFVHSFA 154 + LG+C GE + G + H G V LF+G+ +EG+ + S Sbjct: 75 IPVLGICYGEQAMADQLGGKVEAGHHREFGRAEVEVVKPAALFEGVWQEGQRYLVWMSHG 134 Query: 155 -----MPVGDYTIAECEYGNSFTAAVQSGNYYGVQFHPE-RSSKAGAKLIQNFL 202 +P G IA+ E A +S +YGVQFHPE + GA+L++NF+ Sbjct: 135 DRVTQLPAGFEVIAQSENAPFAAIADESRKFYGVQFHPEVVHTPQGAQLLRNFV 188 Lambda K H 0.317 0.136 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 217 Number of extensions: 15 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 204 Length of database: 515 Length adjustment: 28 Effective length of query: 176 Effective length of database: 487 Effective search space: 85712 Effective search space used: 85712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory